bioimagesUnknownhttps://www.ebi.ac.uk/biostudies/studies/S-BIAD1288bioimagesSpecimenAnnotationsStudy ComponentorganisationBiosampleAssociationsImage acquisitionSeongyeol ParkTyler RisomAdam KagelChristina CurtisMarleen KokMarc J. van de VijverHugo M. HorlingsFelix HartmannVeerle GeurtsAlea DelmastroLise MangianteKathleen HoulahanMichiel de MaakerManon de GraafRobert TibshiraniTon N. SchumacherIris NederlofYunhao BaiCandace C. LiuChristine Yiweh YehErin McCaffreyChristine CamachoCristina SotomayorLeonie VoorwerkNoah GreenwaldAziz KhanMichael AngeloSricharan Reddy VarraZhicheng MaZumana KhairMarc BosseDaisy DingCami SowersJolene RanekHadeesha PiyadasaAlex KongfalseTemporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibitionImmune checkpoint inhibition (ICI) has fundamentally changed cancer treatment. However, only a minority of patients with metastatic triple negative breast cancer (TNBC) benefit from ICI, and our understanding of the determinants of response is limited. To better understand the factors influencing patient outcome, we assembled a longitudinal cohort with tissue from the primary tumor, pre-treatment metastatic tumor, and on-treatment metastatic tumor from 117 patients treated with ICI (nivolumab) in the phase II TONIC trial. We used highly multiplexed imaging to quantify the subcellular localization of 37 proteins in each tumor. To extract meaningful information from the imaging data, we developed SpaceCat, a computational pipeline that quantifies features from imaging data such as cell densi2024-09-28T00:00:00Z2024-09-30T21:10:50.527Z2024-07-24T23:02:53.931ZS-BIAD1288